[gmx-users] Lipid bilayer moved apart

shayamra at post.tau.ac.il shayamra at post.tau.ac.il
Sun Jun 28 16:37:18 CEST 2009


Greetings,

Could you perhaps provide details of your energy minimization  
(conjugated? steep? etc.) and perhaps your mdp file for the simulation  
as well.
What kind of pressure couplings did you use? (isotropic? semi-isotropic? etc.)
How much further away did each layer move?

I think it is usually recommended to simulate membranes with  
semi-isotropic pressure coupling, though I am not sure what is the  
cause of the error you are getting with NPT and LINCS.

Regards,
-Shay

Quoting "Bing Bing" <jarbing09 at gmail.com>:

> Dear All,
> I'm simulating a empty membrane (128POPC + 2460 water) , the structure
> obtained from Tielemen's website.
> Thanks for the help from Justin and Mark, the structure had minimized and
> stop at 217steps
>
> Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
>     5.20262e+03    1.01146e+04    4.17230e+03    3.36598e+03    7.50236e+02
>           LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
>     4.01104e+03    8.22333e+03   -1.49543e+04   -1.31978e+05   -1.41296e+05
>       Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
>    -2.52387e+05    0.00000e+00   -2.52387e+05    0.00000e+00    0.00000e+00
>
>
> Steepest Descents converged to Fmax < 1000 in 217 steps
> Potential Energy  = -2.52387473541938e+05
> Maximum force     =  9.30404466610315e+02 on atom 5631
> Norm of force     =  5.34591310731597e+03
>
> The trajectory and energy seems ok.
>
> With this, i proceed with NVT, although by looking at the energy and
> temperature (300K) graph after NVT both looks fine. But when i tried to look
> at the trajectory, i noticed that the upper layer lipid and lower layer
> lapid actually moved further away from each other as compared to the
> starting structure. And i don't know what cause this to happen. Please
> advice.
> Subsequently, i moved on with NPT and it stopped due to LINCS warning as
> below:-
>
> Step 269, time 0.538 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max inf (between atoms 1980 and 1981) rms inf
> bonds that rotated more than 30 degrees:
>
> This mean that some of the atoms in the structure is moving and it is out of
> the cutt-off which being defined, it also said that it might due to the
> reason that the starting structure is not equilibrated or many overlaps. But
> as what i know,
> the structure is well equilibrated. What is the reason for this? Is it
> something which i missed out during NVT or NPT? Please advice.
>
>
> Regards,
> Bing
>





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